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Sodium in PDB 5wki: Crystal Structure of PG90 Tcr-CD1B-Pg Complex

Protein crystallography data

The structure of Crystal Structure of PG90 Tcr-CD1B-Pg Complex, PDB code: 5wki was solved by A.Shahine, S.Gras, J.Rossjohn, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 75.73 / 2.75
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 152.010, 82.970, 90.160, 90.00, 94.88, 90.00
R / Rfree (%) 21.2 / 25.2

Other elements in 5wki:

The structure of Crystal Structure of PG90 Tcr-CD1B-Pg Complex also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of PG90 Tcr-CD1B-Pg Complex (pdb code 5wki). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of PG90 Tcr-CD1B-Pg Complex, PDB code: 5wki:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 5wki

Go back to Sodium Binding Sites List in 5wki
Sodium binding site 1 out of 2 in the Crystal Structure of PG90 Tcr-CD1B-Pg Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of PG90 Tcr-CD1B-Pg Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na307

b:63.5
occ:1.00
O D:ALA184 3.2 66.0 1.0
CB D:ALA184 3.7 65.3 1.0
CD2 D:PHE198 3.8 44.7 1.0
CE2 D:PHE198 3.8 47.2 1.0
CG D:PHE198 3.9 43.5 1.0
CZ D:PHE198 3.9 45.4 1.0
CA D:ALA184 4.0 64.6 1.0
C D:ALA184 4.0 66.1 1.0
CD1 D:PHE198 4.0 46.0 1.0
CE1 D:PHE198 4.1 46.7 1.0
CB D:PHE198 4.6 42.7 1.0

Sodium binding site 2 out of 2 in 5wki

Go back to Sodium Binding Sites List in 5wki
Sodium binding site 2 out of 2 in the Crystal Structure of PG90 Tcr-CD1B-Pg Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of PG90 Tcr-CD1B-Pg Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na303

b:62.1
occ:1.00
O E:GLY3 3.0 46.5 1.0
O E:ASP24 4.0 38.7 1.0
O E:PRO25 4.0 38.1 1.0
C E:GLY3 4.2 46.4 1.0
OG E:SER5 4.3 41.5 1.0
C E:PRO25 4.5 38.6 1.0
CG E:ASP24 4.7 42.2 1.0
C E:ASP24 4.7 38.8 1.0
OD2 E:ASP24 4.8 36.0 1.0
N E:SER5 4.8 31.4 1.0
CB E:ASP24 4.8 34.6 1.0
CB E:SER5 4.9 33.7 1.0
N E:GLY3 4.9 50.0 1.0
CA E:ILE26 4.9 35.5 1.0
N E:ILE26 5.0 35.7 1.0

Reference:

A.Shahine, I.Van Rhijn, T.Y.Cheng, S.Iwany, S.Gras, D.B.Moody, J.Rossjohn. A Molecular Basis of Human T Cell Receptor Autoreactivity Toward Self-Phospholipids. Sci Immunol V. 2 2017.
ISSN: ESSN 2470-9468
PubMed: 29054999
DOI: 10.1126/SCIIMMUNOL.AAO1384
Page generated: Tue Oct 8 01:02:48 2024

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